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     1 #!/usr/bin/env python
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     2 # -*- coding: utf-8 -*-
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     3 #
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     4 # riboplot documentation build configuration file, created by
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     5 # sphinx-quickstart on Tue Jul  9 22:26:36 2013.
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     6 #
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     7 # This file is execfile()d with the current directory set to its
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     8 # containing dir.
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     9 #
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    10 # Note that not all possible configuration values are present in this
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    11 # autogenerated file.
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    12 #
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    13 # All configuration values have a default; values that are commented out
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    14 # serve to show the default.
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    15 
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    16 import sys
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    17 import os
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    18 
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    19 # If extensions (or modules to document with autodoc) are in another
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    20 # directory, add these directories to sys.path here. If the directory is
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    21 # relative to the documentation root, use os.path.abspath to make it
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    22 # absolute, like shown here.
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    23 #sys.path.insert(0, os.path.abspath('.'))
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    24 
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    25 # Get the project root dir, which is the parent dir of this
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    26 cwd = os.getcwd()
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    27 project_root = os.path.dirname(cwd)
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    28 
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    29 # Insert the project root dir as the first element in the PYTHONPATH.
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    30 # This lets us ensure that the source package is imported, and that its
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    31 # version is used.
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    32 sys.path.insert(0, project_root)
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    33 
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    34 import riboplot
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    35 
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    36 # -- General configuration ---------------------------------------------
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    37 
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    38 # If your documentation needs a minimal Sphinx version, state it here.
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    39 #needs_sphinx = '1.0'
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    40 
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    41 # Add any Sphinx extension module names here, as strings. They can be
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    42 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
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    43 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
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    44 
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    45 # Add any paths that contain templates here, relative to this directory.
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    46 templates_path = ['_templates']
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    47 
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    48 # The suffix of source filenames.
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    49 source_suffix = '.rst'
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    50 
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    51 # The encoding of source files.
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    52 #source_encoding = 'utf-8-sig'
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    53 
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    54 # The master toctree document.
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    55 master_doc = 'index'
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    56 
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    57 # General information about the project.
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    58 project = u'RiboPlot'
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    59 copyright = u'2015, Vimalkumar Velayudhan'
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    60 
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    61 # The version info for the project you're documenting, acts as replacement
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    62 # for |version| and |release|, also used in various other places throughout
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    63 # the built documents.
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    64 #
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    65 # The short X.Y version.
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    66 version = riboplot.__version__
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    67 # The full version, including alpha/beta/rc tags.
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    68 release = riboplot.__version__
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    69 
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    70 # The language for content autogenerated by Sphinx. Refer to documentation
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    71 # for a list of supported languages.
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    72 #language = None
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    73 
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    74 # There are two options for replacing |today|: either, you set today to
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    75 # some non-false value, then it is used:
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    76 #today = ''
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    77 # Else, today_fmt is used as the format for a strftime call.
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    78 #today_fmt = '%B %d, %Y'
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    79 
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    80 # List of patterns, relative to source directory, that match files and
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    81 # directories to ignore when looking for source files.
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    82 exclude_patterns = ['_build']
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    83 
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    84 # The reST default role (used for this markup: `text`) to use for all
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    85 # documents.
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    86 #default_role = None
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    87 
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    88 # If true, '()' will be appended to :func: etc. cross-reference text.
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    89 #add_function_parentheses = True
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    90 
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    91 # If true, the current module name will be prepended to all description
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    92 # unit titles (such as .. function::).
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    93 #add_module_names = True
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    94 
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    95 # If true, sectionauthor and moduleauthor directives will be shown in the
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    96 # output. They are ignored by default.
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    97 #show_authors = False
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    98 
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    99 # The name of the Pygments (syntax highlighting) style to use.
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   100 pygments_style = 'sphinx'
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   101 
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   102 # A list of ignored prefixes for module index sorting.
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   103 #modindex_common_prefix = []
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   104 
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   105 # If true, keep warnings as "system message" paragraphs in the built
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   106 # documents.
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   107 #keep_warnings = False
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   108 
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   109 
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   110 # -- Options for HTML output -------------------------------------------
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   111 
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   112 # The theme to use for HTML and HTML Help pages.  See the documentation for
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   113 # a list of builtin themes.
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   114 html_theme = 'alabaster'
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   115 
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   116 # Theme options are theme-specific and customize the look and feel of a
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   117 # theme further.  For a list of options available for each theme, see the
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   118 # documentation.
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   119 #html_theme_options = {}
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   120 html_theme_options = {
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   121         'font_family': '"Source Sans Pro", Ubuntu, sans-serif',
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   122         'head_font_family': 'Cabin, Ubuntu, sans-serif',
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   123         'code_font_family': '"Source Code Pro", "Ubuntu Mono", monospace',
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   124         'code_font_size': '0.8em',
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   125         'pre_bg': '#f9f9f9', 'note_bg': '#e6f7ff', 'note_border': '#ccefff',
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   126         'sidebar_list': '#777777', 'body_text': '#515151', 'show_powered_by': False}
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   127 
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   128 
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   129 # Add any paths that contain custom themes here, relative to this directory.
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   130 #html_theme_path = []
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   131 
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   132 # The name for this set of Sphinx documents.  If None, it defaults to
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   133 # "<project> v<release> documentation".
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   134 #html_title = None
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   135 
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   136 # A shorter title for the navigation bar.  Default is the same as
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   137 # html_title.
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   138 #html_short_title = None
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   139 
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   140 # The name of an image file (relative to this directory) to place at the
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   141 # top of the sidebar.
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   142 #html_logo = None
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   143 
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   144 # The name of an image file (within the static path) to use as favicon
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   145 # of the docs.  This file should be a Windows icon file (.ico) being
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   146 # 16x16 or 32x32 pixels large.
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   147 #html_favicon = None
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   148 
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   149 # Add any paths that contain custom static files (such as style sheets)
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   150 # here, relative to this directory. They are copied after the builtin
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   151 # static files, so a file named "default.css" will overwrite the builtin
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   152 # "default.css".
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   153 html_static_path = ['_static']
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   154 
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   155 # If not '', a 'Last updated on:' timestamp is inserted at every page
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   156 # bottom, using the given strftime format.
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   157 #html_last_updated_fmt = '%b %d, %Y'
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   158 
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   159 # If true, SmartyPants will be used to convert quotes and dashes to
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   160 # typographically correct entities.
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   161 #html_use_smartypants = True
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   162 
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   163 # Custom sidebar templates, maps document names to template names.
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   164 #html_sidebars = {}
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   165 
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   166 # Additional templates that should be rendered to pages, maps page names
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   167 # to template names.
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   168 #html_additional_pages = {}
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   169 
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   170 # If false, no module index is generated.
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   171 #html_domain_indices = True
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   172 
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   173 # If false, no index is generated.
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   174 #html_use_index = True
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   175 
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   176 # If true, the index is split into individual pages for each letter.
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   177 #html_split_index = False
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   178 
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   179 # If true, links to the reST sources are added to the pages.
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   180 #html_show_sourcelink = True
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   181 
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   182 # If true, "Created using Sphinx" is shown in the HTML footer.
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   183 # Default is True.
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   184 #html_show_sphinx = True
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   185 
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   186 # If true, "(C) Copyright ..." is shown in the HTML footer.
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   187 # Default is True.
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   188 #html_show_copyright = True
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   189 
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   190 # If true, an OpenSearch description file will be output, and all pages
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   191 # will contain a <link> tag referring to it.  The value of this option
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   192 # must be the base URL from which the finished HTML is served.
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   193 #html_use_opensearch = ''
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   194 
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   195 # This is the file name suffix for HTML files (e.g. ".xhtml").
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   196 #html_file_suffix = None
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   197 
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   198 # Output file base name for HTML help builder.
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   199 htmlhelp_basename = 'riboplotdoc'
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   200 
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   201 
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   202 # -- Options for LaTeX output ------------------------------------------
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   203 
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   204 latex_elements = {
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   205     # The paper size ('letterpaper' or 'a4paper').
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   206     #'papersize': 'letterpaper',
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   207 
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   208     # The font size ('10pt', '11pt' or '12pt').
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   209     #'pointsize': '10pt',
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   210 
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   211     # Additional stuff for the LaTeX preamble.
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   212     #'preamble': '',
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   213 }
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   214 
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   215 # Grouping the document tree into LaTeX files. List of tuples
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   216 # (source start file, target name, title, author, documentclass
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   217 # [howto/manual]).
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   218 latex_documents = [
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   219     ('index', 'riboplot.tex',
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   220      u'RiboPlot Documentation',
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   221      u'Vimalkumar Velayudhan', 'manual'),
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   222 ]
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   223 
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   224 # The name of an image file (relative to this directory) to place at
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   225 # the top of the title page.
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   226 #latex_logo = None
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   227 
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   228 # For "manual" documents, if this is true, then toplevel headings
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   229 # are parts, not chapters.
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   230 #latex_use_parts = False
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   231 
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   232 # If true, show page references after internal links.
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   233 #latex_show_pagerefs = False
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   234 
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   235 # If true, show URL addresses after external links.
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   236 #latex_show_urls = False
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   237 
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   238 # Documents to append as an appendix to all manuals.
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   239 #latex_appendices = []
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   240 
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   241 # If false, no module index is generated.
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   242 #latex_domain_indices = True
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   243 
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   244 
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   245 # -- Options for manual page output ------------------------------------
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   246 
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   247 # One entry per manual page. List of tuples
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   248 # (source start file, name, description, authors, manual section).
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   249 man_pages = [
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   250     ('index', 'riboplot',
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   251      u'RiboPlot Documentation',
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   252      [u'Vimalkumar Velayudhan'], 1)
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   253 ]
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   254 
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   255 # If true, show URL addresses after external links.
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   256 #man_show_urls = False
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   257 
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   258 
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   259 # -- Options for Texinfo output ----------------------------------------
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   260 
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   261 # Grouping the document tree into Texinfo files. List of tuples
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   262 # (source start file, target name, title, author,
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   263 #  dir menu entry, description, category)
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   264 texinfo_documents = [
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   265     ('index', 'riboplot',
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   266      u'RiboPlot Documentation',
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   267      u'Vimalkumar Velayudhan',
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   268      'riboplot',
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   269      'One line description of project.',
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   270      'Miscellaneous'),
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   271 ]
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   272 
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   273 # Documents to append as an appendix to all manuals.
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   274 #texinfo_appendices = []
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   275 
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   276 # If false, no module index is generated.
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   277 #texinfo_domain_indices = True
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   278 
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   279 # How to display URL addresses: 'footnote', 'no', or 'inline'.
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   280 #texinfo_show_urls = 'footnote'
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   281 
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   282 # If true, do not generate a @detailmenu in the "Top" node's menu.
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7
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Bugfix: (ribocounts) Read length was sent as rnafile argument in check_optional_arguments
  
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   283 #texinfo_no_detailmenu = False
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